n_crassa.md

Build a 3D genome model for Neurospora crassa

The HiC data are from Galazka et al. 2016 (SRA ID : SRX1099807) and the ChipSeq data from Jamieson et al. 2015 (SRA ID : SRR2026390) and Basenko et al. 2015 (SRA ID : SRR2036168).

Download and prepare the reference genome sequence

bash examples/n_crassa_prepare_genome.sh

Build 3D genome model

snakemake --profile smk_profile -j 4 --configfile examples/n_crassa_WT.yml

See output file 3DGB_n_crassa_WT/structure/50000/structure_cleaned.pdb that should be equivalent to examples/structure_cleaned.pdb.

Without taking into account the time to download fastq files, the 3D genome models generation should take about 40 minutes with 4 Intel i7-8665U cores at 1.90 GHz.

Map ChipSeq values to the 3D model

python scripts/map_parameter.py --pdb "3DGB_n_crassa_WT/structure/50000/structure_cleaned.pdb" --BedGraph "examples/n_crassa.bedgraph" --output "3DGB_n_crassa_WT/structure/50000/structure_with_parameter.pdb"

See output file ./3DGB_n_crassa_WT/structure/50000/structure_with_parameter.pdb that should be equivalent to examples/structure_with_parameter.pdb.